quality_control
Programs
These are the programs that need to be installed and included locally.
library(gridExtra)
library(knitr)
library(ggplot2)
#install.packages("fastqcr")
library(fastqcr)
fastqc_install()Only Modify This Chunk
This is the only chunk that needs modification when reusing this script with different datasets. The later chunks produce outputs based on the directory locations listed here.
## assign directory locations
# the full path to the .fast.gz files for each sample:
fq.dir<-"/storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/lil_samples"
# the full path for outputs
qc.dir<-"/storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control"Run fastqc
Only run this code once when first working on the files. The outputs are a html and a zip file for each sample. When these are produced, you don’t need to produce them again if you rerun the code further down. This is why this chunk is temporarily commented out.
#fastqc(fq.dir = fq.dir, # FASTQ files directory
# qc.dir = qc.dir, # Results directory
# threads = 4 # Number of threads
# )# list the files in the output directory to ensure success (if you want)
#list.files(qc.dir)
# a better way to check success is to compare the number of files
# first list the number of samples files
length(list.files(fq.dir, pattern = "*.fastq.gz"))## [1] 109# and see if it matches the number of output zip files
length(list.files(qc.dir, pattern = "*.zip"))## [1] 109Quality Plots for Each Sample
# create a vector with the samples names, taken from the output files
samps<-list.files(qc.dir, full.names = T, pattern = "*.zip")
#plot qc test results for each sample
for (i in samps){
#read info for given sample from the .zip file generated in the previous step
samp.info <- qc_read(i)
#open blank list to hold qc visualizations for the given sample
plot<-list()
#do qc for the given sample
plot[[1]]<-qc_plot(samp.info, "Basic statistics")
plot[[2]]<-qc_plot(samp.info, "Per sequence quality scores")
plot[[3]]<-qc_plot(samp.info, "Sequence duplication levels")
#visualize tables
print(paste0("QC results for sample ", gsub(".*/", "", i)))
cat('\n')
print(kable(plot[[1]]))
cat('\n')
#visualize plots
grid.arrange(plot[[2]],plot[[3]],
ncol=2)
#clear plot to hold info for next sample
rm(plot)
}## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_127_fastqc.zip## [1] "QC results for sample Hlil_127_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_127.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |71024 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |54 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_130_fastqc.zip
## [1] "QC results for sample Hlil_130_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_130.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |2003627 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |54 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_132_fastqc.zip
## [1] "QC results for sample Hlil_132_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_132.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |2236334 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |54 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_135_fastqc.zip
## [1] "QC results for sample Hlil_135_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_135.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |545242 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |56 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_137_fastqc.zip
## [1] "QC results for sample Hlil_137_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_137.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1572141 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_143_fastqc.zip
## [1] "QC results for sample Hlil_143_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_143.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1490633 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_145_fastqc.zip
## [1] "QC results for sample Hlil_145_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_145.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1446751 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_146_fastqc.zip
## [1] "QC results for sample Hlil_146_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_146.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |816769 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |57 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_147_fastqc.zip
## [1] "QC results for sample Hlil_147_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_147.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |4651854 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |54 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_148_fastqc.zip
## [1] "QC results for sample Hlil_148_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_148.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1888604 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |55 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_150_fastqc.zip
## [1] "QC results for sample Hlil_150_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_150.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |3066462 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |55 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_152_fastqc.zip
## [1] "QC results for sample Hlil_152_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_152.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |2712705 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_153_fastqc.zip
## [1] "QC results for sample Hlil_153_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_153.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |2591356 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_154_fastqc.zip
## [1] "QC results for sample Hlil_154_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_154.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1674461 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_155_fastqc.zip
## [1] "QC results for sample Hlil_155_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_155.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |914366 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |54 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_156_fastqc.zip
## [1] "QC results for sample Hlil_156_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_156.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1307126 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |58 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_157_fastqc.zip
## [1] "QC results for sample Hlil_157_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_157.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1089297 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_158_fastqc.zip
## [1] "QC results for sample Hlil_158_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_158.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1541016 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |56 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_159_fastqc.zip
## [1] "QC results for sample Hlil_159_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_159.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1734326 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |56 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_160_fastqc.zip
## [1] "QC results for sample Hlil_160_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_160.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1083021 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |55 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_161_fastqc.zip
## [1] "QC results for sample Hlil_161_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_161.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1866482 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_162_fastqc.zip
## [1] "QC results for sample Hlil_162_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_162.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1654937 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_163_fastqc.zip
## [1] "QC results for sample Hlil_163_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_163.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |2633376 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |54 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_164_fastqc.zip
## [1] "QC results for sample Hlil_164_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_164.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |2837977 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_165_fastqc.zip
## [1] "QC results for sample Hlil_165_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_165.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |4609865 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_166_fastqc.zip
## [1] "QC results for sample Hlil_166_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_166.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |2830748 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_168_fastqc.zip
## [1] "QC results for sample Hlil_168_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_168.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1307980 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_169_fastqc.zip
## [1] "QC results for sample Hlil_169_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_169.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |4133873 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_173_fastqc.zip
## [1] "QC results for sample Hlil_173_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_173.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |2630072 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_174_fastqc.zip
## [1] "QC results for sample Hlil_174_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_174.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |3683216 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_175_fastqc.zip
## [1] "QC results for sample Hlil_175_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_175.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1946397 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_176_fastqc.zip
## [1] "QC results for sample Hlil_176_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_176.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |2606430 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_177_fastqc.zip
## [1] "QC results for sample Hlil_177_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_177.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |2108701 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_178_fastqc.zip
## [1] "QC results for sample Hlil_178_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_178.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |2648953 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_179_fastqc.zip
## [1] "QC results for sample Hlil_179_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_179.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |2642622 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_180_fastqc.zip
## [1] "QC results for sample Hlil_180_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_180.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |3374155 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_181_fastqc.zip
## [1] "QC results for sample Hlil_181_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_181.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |421595 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_182_fastqc.zip
## [1] "QC results for sample Hlil_182_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_182.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |2317930 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_183_fastqc.zip
## [1] "QC results for sample Hlil_183_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_183.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |802234 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_184_fastqc.zip
## [1] "QC results for sample Hlil_184_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_184.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |650295 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |55 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_185_fastqc.zip
## [1] "QC results for sample Hlil_185_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_185.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1025935 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_186_fastqc.zip
## [1] "QC results for sample Hlil_186_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_186.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |551799 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_188_fastqc.zip
## [1] "QC results for sample Hlil_188_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_188.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1198003 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_189_fastqc.zip
## [1] "QC results for sample Hlil_189_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_189.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |415025 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_190_fastqc.zip
## [1] "QC results for sample Hlil_190_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_190.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1063764 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_191_fastqc.zip
## [1] "QC results for sample Hlil_191_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_191.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1174120 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_192_fastqc.zip
## [1] "QC results for sample Hlil_192_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_192.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |111094 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_193_fastqc.zip
## [1] "QC results for sample Hlil_193_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_193.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1665511 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_195_fastqc.zip
## [1] "QC results for sample Hlil_195_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_195.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |217625 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_196_fastqc.zip
## [1] "QC results for sample Hlil_196_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_196.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |2097876 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_197_fastqc.zip
## [1] "QC results for sample Hlil_197_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_197.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1205600 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_198_fastqc.zip
## [1] "QC results for sample Hlil_198_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_198.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |970559 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_199_fastqc.zip
## [1] "QC results for sample Hlil_199_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_199.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1034547 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_200_fastqc.zip
## [1] "QC results for sample Hlil_200_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_200.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1010091 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_201_fastqc.zip
## [1] "QC results for sample Hlil_201_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_201.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |627998 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_202_fastqc.zip
## [1] "QC results for sample Hlil_202_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_202.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1274612 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_203_fastqc.zip
## [1] "QC results for sample Hlil_203_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_203.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1391584 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_204_fastqc.zip
## [1] "QC results for sample Hlil_204_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_204.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |741691 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_205_fastqc.zip
## [1] "QC results for sample Hlil_205_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_205.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1569870 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_206_fastqc.zip
## [1] "QC results for sample Hlil_206_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_206.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |298080 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |57 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_207_fastqc.zip
## [1] "QC results for sample Hlil_207_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_207.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |2746727 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_208_fastqc.zip
## [1] "QC results for sample Hlil_208_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_208.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |219015 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_209_fastqc.zip
## [1] "QC results for sample Hlil_209_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_209.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1626053 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_210_fastqc.zip
## [1] "QC results for sample Hlil_210_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_210.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1609485 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_211_fastqc.zip
## [1] "QC results for sample Hlil_211_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_211.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1175159 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_212_fastqc.zip
## [1] "QC results for sample Hlil_212_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_212.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |259017 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_213_fastqc.zip
## [1] "QC results for sample Hlil_213_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_213.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1411565 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_214_fastqc.zip
## [1] "QC results for sample Hlil_214_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_214.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |2057978 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_215_fastqc.zip
## [1] "QC results for sample Hlil_215_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_215.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |738322 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_216_fastqc.zip
## [1] "QC results for sample Hlil_216_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_216.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |958785 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_217_fastqc.zip
## [1] "QC results for sample Hlil_217_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_217.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |307499 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_218_fastqc.zip
## [1] "QC results for sample Hlil_218_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_218.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |617199 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_219_fastqc.zip
## [1] "QC results for sample Hlil_219_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_219.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |2358499 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_220_fastqc.zip
## [1] "QC results for sample Hlil_220_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_220.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |939542 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_221_fastqc.zip
## [1] "QC results for sample Hlil_221_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_221.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |448543 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_224_fastqc.zip
## [1] "QC results for sample Hlil_224_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_224.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1325242 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_225_fastqc.zip
## [1] "QC results for sample Hlil_225_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_225.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |481073 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_226_fastqc.zip
## [1] "QC results for sample Hlil_226_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_226.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1145517 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_227_fastqc.zip
## [1] "QC results for sample Hlil_227_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_227.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |236877 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_228_fastqc.zip
## [1] "QC results for sample Hlil_228_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_228.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |595712 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_229_fastqc.zip
## [1] "QC results for sample Hlil_229_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_229.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |676317 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_230_fastqc.zip
## [1] "QC results for sample Hlil_230_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_230.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |129535 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |54 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_231_fastqc.zip
## [1] "QC results for sample Hlil_231_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_231.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1238697 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_232_fastqc.zip
## [1] "QC results for sample Hlil_232_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_232.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |743479 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_233_fastqc.zip
## [1] "QC results for sample Hlil_233_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_233.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1065394 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_234_fastqc.zip
## [1] "QC results for sample Hlil_234_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_234.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |114929 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_235_fastqc.zip
## [1] "QC results for sample Hlil_235_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_235.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1700592 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_236_fastqc.zip
## [1] "QC results for sample Hlil_236_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_236.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |347630 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_237_fastqc.zip
## [1] "QC results for sample Hlil_237_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_237.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |209300 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_238_fastqc.zip
## [1] "QC results for sample Hlil_238_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_238.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |488277 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_239_fastqc.zip
## [1] "QC results for sample Hlil_239_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_239.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |333793 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_240_fastqc.zip
## [1] "QC results for sample Hlil_240_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_240.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |655178 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_241_fastqc.zip
## [1] "QC results for sample Hlil_241_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_241.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |674262 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_242_fastqc.zip
## [1] "QC results for sample Hlil_242_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_242.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |820807 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_243_fastqc.zip
## [1] "QC results for sample Hlil_243_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_243.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |2356281 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_244_fastqc.zip
## [1] "QC results for sample Hlil_244_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_244.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1045211 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_245_fastqc.zip
## [1] "QC results for sample Hlil_245_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_245.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |622481 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_246_fastqc.zip
## [1] "QC results for sample Hlil_246_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_246.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1180373 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_247_fastqc.zip
## [1] "QC results for sample Hlil_247_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_247.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1142556 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_248_fastqc.zip
## [1] "QC results for sample Hlil_248_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_248.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1005973 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |57 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_NBG_351_fastqc.zip
## [1] "QC results for sample Hlil_NBG_351_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_NBG_351.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1644600 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_NC_167_fastqc.zip
## [1] "QC results for sample Hlil_NC_167_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_NC_167.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |3093287 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_NC_170_fastqc.zip
## [1] "QC results for sample Hlil_NC_170_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_NC_170.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1123578 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_NC_171_fastqc.zip
## [1] "QC results for sample Hlil_NC_171_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_NC_171.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |5068513 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_NC_172_fastqc.zip
## [1] "QC results for sample Hlil_NC_172_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_NC_172.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |3926228 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |51 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_NTBG_260_fastqc.zip
## [1] "QC results for sample Hlil_NTBG_260_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_NTBG_260.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |1749198 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |52 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_W_222_fastqc.zip
## [1] "QC results for sample Hlil_W_222_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_W_222.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |753330 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_W_223_fastqc.zip
## [1] "QC results for sample Hlil_W_223_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_W_223.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |716338 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |53 |## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_WBG_226_fastqc.zip
## [1] "QC results for sample Hlil_WBG_226_fastqc.zip"
##
##
##
## |Measure |Value |
## |:---------------------------------|:-----------------------|
## |Filename |Hlil_WBG_226.fastq.gz |
## |File type |Conventional base calls |
## |Encoding |Sanger / Illumina 1.9 |
## |Total Sequences |324748 |
## |Sequences flagged as poor quality |0 |
## |Sequence length |36 |
## |%GC |54 |
Aggregate Report
This is an aggregate report; it produces a table with some summary stats for each sample.
#aggregate the reports by pointing this function to the folder holding the output files
qc <- qc_aggregate(qc.dir, progressbar = F)## Warning: `select_()` is deprecated as of dplyr 0.7.0.
## Please use `select()` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.#stats per sample
knitr::kable(qc_stats(qc))| sample | pct.dup | pct.gc | tot.seq | seq.length |
|---|---|---|---|---|
| Hlil_127 | 66.94 | 54 | 71024 | 36 |
| Hlil_130 | 94.07 | 54 | 2003627 | 36 |
| Hlil_132 | 94.73 | 54 | 2236334 | 36 |
| Hlil_135 | 84.20 | 56 | 545242 | 36 |
| Hlil_137 | 94.61 | 53 | 1572141 | 36 |
| Hlil_143 | 93.86 | 53 | 1490633 | 36 |
| Hlil_145 | 90.38 | 53 | 1446751 | 36 |
| Hlil_146 | 85.70 | 57 | 816769 | 36 |
| Hlil_147 | 95.88 | 54 | 4651854 | 36 |
| Hlil_148 | 89.46 | 55 | 1888604 | 36 |
| Hlil_150 | 92.17 | 55 | 3066462 | 36 |
| Hlil_152 | 94.50 | 52 | 2712705 | 36 |
| Hlil_153 | 94.25 | 52 | 2591356 | 36 |
| Hlil_154 | 91.75 | 52 | 1674461 | 36 |
| Hlil_155 | 90.62 | 54 | 914366 | 36 |
| Hlil_156 | 84.17 | 58 | 1307126 | 36 |
| Hlil_157 | 88.71 | 52 | 1089297 | 36 |
| Hlil_158 | 90.83 | 56 | 1541016 | 36 |
| Hlil_159 | 92.05 | 56 | 1734326 | 36 |
| Hlil_160 | 87.28 | 55 | 1083021 | 36 |
| Hlil_161 | 92.48 | 52 | 1866482 | 36 |
| Hlil_162 | 92.66 | 53 | 1654937 | 36 |
| Hlil_163 | 94.44 | 54 | 2633376 | 36 |
| Hlil_164 | 95.02 | 53 | 2837977 | 36 |
| Hlil_165 | 97.28 | 51 | 4609865 | 36 |
| Hlil_166 | 95.77 | 52 | 2830748 | 36 |
| Hlil_168 | 94.10 | 53 | 1307980 | 36 |
| Hlil_169 | 96.47 | 53 | 4133873 | 36 |
| Hlil_173 | 95.10 | 53 | 2630072 | 36 |
| Hlil_174 | 96.51 | 52 | 3683216 | 36 |
| Hlil_175 | 95.80 | 53 | 1946397 | 36 |
| Hlil_176 | 96.59 | 52 | 2606430 | 36 |
| Hlil_177 | 94.48 | 52 | 2108701 | 36 |
| Hlil_178 | 94.89 | 53 | 2648953 | 36 |
| Hlil_179 | 95.44 | 52 | 2642622 | 36 |
| Hlil_180 | 96.92 | 51 | 3374155 | 36 |
| Hlil_181 | 87.72 | 52 | 421595 | 36 |
| Hlil_182 | 93.99 | 52 | 2317930 | 36 |
| Hlil_183 | 91.57 | 52 | 802234 | 36 |
| Hlil_184 | 83.34 | 55 | 650295 | 36 |
| Hlil_185 | 90.23 | 53 | 1025935 | 36 |
| Hlil_186 | 89.42 | 53 | 551799 | 36 |
| Hlil_188 | 89.68 | 53 | 1198003 | 36 |
| Hlil_189 | 87.94 | 53 | 415025 | 36 |
| Hlil_190 | 91.35 | 52 | 1063764 | 36 |
| Hlil_191 | 91.45 | 52 | 1174120 | 36 |
| Hlil_192 | 73.92 | 53 | 111094 | 36 |
| Hlil_193 | 92.23 | 52 | 1665511 | 36 |
| Hlil_195 | 83.38 | 53 | 217625 | 36 |
| Hlil_196 | 93.92 | 51 | 2097876 | 36 |
| Hlil_197 | 91.69 | 51 | 1205600 | 36 |
| Hlil_198 | 92.49 | 52 | 970559 | 36 |
| Hlil_199 | 91.70 | 51 | 1034547 | 36 |
| Hlil_200 | 91.14 | 51 | 1010091 | 36 |
| Hlil_201 | 90.01 | 53 | 627998 | 36 |
| Hlil_202 | 91.74 | 51 | 1274612 | 36 |
| Hlil_203 | 92.50 | 51 | 1391584 | 36 |
| Hlil_204 | 88.54 | 52 | 741691 | 36 |
| Hlil_205 | 91.95 | 51 | 1569870 | 36 |
| Hlil_206 | 77.65 | 57 | 298080 | 36 |
| Hlil_207 | 94.83 | 52 | 2746727 | 36 |
| Hlil_208 | 79.84 | 53 | 219015 | 36 |
| Hlil_209 | 92.25 | 53 | 1626053 | 36 |
| Hlil_210 | 91.61 | 52 | 1609485 | 36 |
| Hlil_211 | 91.48 | 51 | 1175159 | 36 |
| Hlil_212 | 82.83 | 53 | 259017 | 36 |
| Hlil_213 | 91.52 | 51 | 1411565 | 36 |
| Hlil_214 | 93.27 | 51 | 2057978 | 36 |
| Hlil_215 | 90.79 | 52 | 738322 | 36 |
| Hlil_216 | 90.78 | 52 | 958785 | 36 |
| Hlil_217 | 85.51 | 53 | 307499 | 36 |
| Hlil_218 | 91.41 | 52 | 617199 | 36 |
| Hlil_219 | 94.19 | 51 | 2358499 | 36 |
| Hlil_220 | 89.66 | 53 | 939542 | 36 |
| Hlil_221 | 90.25 | 51 | 448543 | 36 |
| Hlil_224 | 92.59 | 51 | 1325242 | 36 |
| Hlil_225 | 89.79 | 53 | 481073 | 36 |
| Hlil_226 | 91.55 | 52 | 1145517 | 36 |
| Hlil_227 | 85.54 | 52 | 236877 | 36 |
| Hlil_228 | 89.69 | 52 | 595712 | 36 |
| Hlil_229 | 91.30 | 51 | 676317 | 36 |
| Hlil_230 | 81.05 | 54 | 129535 | 36 |
| Hlil_231 | 93.36 | 51 | 1238697 | 36 |
| Hlil_232 | 92.02 | 52 | 743479 | 36 |
| Hlil_233 | 92.54 | 51 | 1065394 | 36 |
| Hlil_234 | 79.91 | 52 | 114929 | 36 |
| Hlil_235 | 92.99 | 51 | 1700592 | 36 |
| Hlil_236 | 88.37 | 52 | 347630 | 36 |
| Hlil_237 | 84.20 | 52 | 209300 | 36 |
| Hlil_238 | 90.44 | 52 | 488277 | 36 |
| Hlil_239 | 88.90 | 53 | 333793 | 36 |
| Hlil_240 | 87.67 | 52 | 655178 | 36 |
| Hlil_241 | 91.34 | 51 | 674262 | 36 |
| Hlil_242 | 91.77 | 53 | 820807 | 36 |
| Hlil_243 | 93.98 | 52 | 2356281 | 36 |
| Hlil_244 | 90.42 | 52 | 1045211 | 36 |
| Hlil_245 | 89.22 | 52 | 622481 | 36 |
| Hlil_246 | 91.51 | 52 | 1180373 | 36 |
| Hlil_247 | 90.83 | 52 | 1142556 | 36 |
| Hlil_248 | 83.95 | 57 | 1005973 | 36 |
| Hlil_NBG_351 | 94.01 | 51 | 1644600 | 36 |
| Hlil_NC_167 | 95.93 | 53 | 3093287 | 36 |
| Hlil_NC_170 | 93.56 | 53 | 1123578 | 36 |
| Hlil_NC_171 | 97.12 | 53 | 5068513 | 36 |
| Hlil_NC_172 | 97.00 | 51 | 3926228 | 36 |
| Hlil_NTBG_260 | 94.34 | 52 | 1749198 | 36 |
| Hlil_W_222 | 90.11 | 53 | 753330 | 36 |
| Hlil_W_223 | 90.70 | 53 | 716338 | 36 |
| Hlil_WBG_226 | 79.69 | 54 | 324748 | 36 |
Summary Figures for All Samples
In the following figures: - the solid red line = median sample value - the dashed red line = 10% of median value
#save stats info as an object
stats.info<-qc_stats(qc)
#make tot.seq numeric
stats.info$tot.seq<-as.numeric(stats.info$tot.seq)
#make histogram of number of sequence reads for each sample
ggplot(stats.info, aes(x=tot.seq))+
geom_histogram(color="black", fill="white", bins=20)+
geom_vline(aes(xintercept=median(tot.seq)), color = "red")+
geom_vline(aes(xintercept=median(tot.seq)*.1), color = "red", lty=14)+
theme_classic()+
xlab("Number of sequencing reads")
#solid red line = median sample value
#dashed red line = 10% of median sample value
ggplot(stats.info, aes(x=tot.seq))+
geom_histogram(color="black", fill="white", bins=200)+
geom_vline(aes(xintercept=median(tot.seq)), color = "red")+
geom_vline(aes(xintercept=median(tot.seq)*.1), color = "red", lty=14)+
theme_classic()+
xlab("Number of sequencing reads")
Samples to Drop
The samples to drop are selected as having less than 10% of the median reads.
#show me the samples that have less than 10% of the number of reads as the median sample from this experiment (these should be dropped immediately)
print(paste("Median sample contains", median(stats.info$tot.seq), "reads. The following samples contain less than", median(stats.info$tot.seq)*.1, "reads (10% of the median), and should likely be dropped"))## [1] "Median sample contains 1175159 reads. The following samples contain less than 117515.9 reads (10% of the median), and should likely be dropped"knitr::kable(stats.info[stats.info$tot.seq < median(stats.info$tot.seq)*.1,])| sample | pct.dup | pct.gc | tot.seq | seq.length |
|---|---|---|---|---|
| Hlil_127 | 66.94 | 54 | 71024 | 36 |
| Hlil_192 | 73.92 | 53 | 111094 | 36 |
| Hlil_234 | 79.91 | 52 | 114929 | 36 |